DOI: 10.18129/B9.bioc.CINdex    

This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see CINdex.

Chromosome Instability Index

Bioconductor version: 3.11

The CINdex package addresses important area of high-throughput genomic analysis. It allows the automated processing and analysis of the experimental DNA copy number data generated by Affymetrix SNP 6.0 arrays or similar high throughput technologies. It calculates the chromosome instability (CIN) index that allows to quantitatively characterize genome-wide DNA copy number alterations as a measure of chromosomal instability. This package calculates not only overall genomic instability, but also instability in terms of copy number gains and losses separately at the chromosome and cytoband level.

Author: Lei Song, Krithika Bhuvaneshwar, Yue Wang, Yuanjian Feng, Ie-Ming Shih, Subha Madhavan, Yuriy Gusev

Maintainer: Yuriy Gusev <yg63 at>

Citation (from within R, enter citation("CINdex")):


To install this package, start R (version "4.0") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:



PDF R Script CINdex Tutorial
PDF R Script Prepare input data for CINdex
PDF   Reference Manual
Text   NEWS


biocViews CopyNumberVariation, Genetics, GenomicVariation, Microarray, Sequencing, Software, aCGH
Version 1.16.0
In Bioconductor since BioC 3.3 (R-3.3) (4.5 years)
License GPL (>= 2)
Depends R (>= 3.3), GenomicRanges
Imports bitops, gplots, grDevices, som, dplyr, gridExtra, png, stringr, S4Vectors, IRanges, GenomeInfoDb, graphics, stats, utils
Suggests knitr, testthat, ReactomePA, RUnit, BiocGenerics, AnnotationHub, rtracklayer, pd.genomewidesnp.6,, biovizBase, TxDb.Hsapiens.UCSC.hg18.knownGene, methods, Biostrings, Homo.sapiens
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